Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
Department of Chemistry, Centre for Analytical Science, Loughborough University, Loughborough LE11 3TU, UK; Synbiochem, Manchester Institute of Biotechnology, University of Manchester, Princess Street, Manchester M1 7DN, UK.
Cell Syst. 2020 Sep 23;11(3):300-314.e8. doi: 10.1016/j.cels.2020.08.007. Epub 2020 Sep 11.
Single-cell gene expression is inherently variable, but how this variability is controlled in response to stimulation remains unclear. Here, we use single-cell RNA-seq and single-molecule mRNA counting (smFISH) to study inducible gene expression in the immune toll-like receptor system. We show that mRNA counts of tumor necrosis factor α conform to a standard stochastic switch model, while transcription of interleukin-1β involves an additional regulatory step resulting in increased heterogeneity. Despite different modes of regulation, systematic analysis of single-cell data for a range of genes demonstrates that the variability in transcript count is linearly constrained by the mean response over a range of conditions. Mathematical modeling of smFISH counts and experimental perturbation of chromatin state demonstrates that linear constraints emerge through modulation of transcriptional bursting along with gene-specific relationships. Overall, our analyses demonstrate that the variability of the inducible single-cell mRNA response is constrained by transcriptional bursting.
单细胞基因表达本质上是可变的，但这种可变性如何响应刺激尚不清楚。在这里，我们使用单细胞 RNA-seq 和单分子 mRNA 计数 (smFISH) 来研究免疫 Toll 样受体系统中的诱导基因表达。我们表明，肿瘤坏死因子 α 的 mRNA 计数符合标准的随机开关模型，而白细胞介素-1β 的转录涉及额外的调节步骤，导致异质性增加。尽管调控方式不同，但对一系列基因的单细胞数据进行系统分析表明，转录本计数的变异性在线性上受到条件范围内平均响应的限制。smFISH 计数的数学建模和染色质状态的实验扰动表明，线性约束是通过转录爆发的调制以及基因特异性关系出现的。总的来说，我们的分析表明，诱导的单细胞 mRNA 反应的可变性受到转录爆发的限制。
